Nagqu, as the center of the ecological barrier area of the Qinghai-Tibet plateau, provides significant ecosystem services for maintaining the ecological security and achieving sustainable development of plateau and the surrounding areas. This paper adopted InVEST and CASA models to evaluate four ecosystem services of Nagqu in 2000, 2010 and 2018, which included water yield, soil retention, carbon sequestration and habitat quality. Then, the spatiotemporal pattern and interrelation of them were analyzed, and the main influencing factors of the spatial heterogeneity of ecosystem services in Nagqu were further revealed by Geodetector. The results showed that 1) from 2000 to 2018, water yield decreased by 35.1%, soil retention decreased by 4.8%, habitat quality was stable, but carbon sequestration increased by 5.6%; 2) From 2000 to 2018, the spatial distribution of water yield, soil retention, and carbon sequestration showed a trend of higher in the southeast and lower in the northwest in Nagqu. Moreover, the areas with high value of habitat quality distributed in the lakes, rivers, and areas with high vegetation coverage. Furthermore, the area of extreme importance and the area of high importance served by ecosystem services in Nagqu accounted for 5.3%-5.4% and 12.3%-13.8%, respectively, which mainly distributed in the central and eastern Nagqu with good hydrothermal and vegetation conditions; 3) There was a mainly synergetic relationship among the four ecosystem services in Nagqu from 2000 to 2018, and the synergy between water yield and soil retention was the strongest; 4) According to the result analyzed by factor detector, the annual precipitation, soil type, and Normalized Difference Vegetation Index (NDVI) had the strongest contributions for the spatial heterogeneity of water yield and carbon sequestration, the spatial heterogeneity of soil retention was mainly affected by slope, and habitat quality was mostly affected by land use type. According to interaction detection, the interaction between land use type and the NDVI had the strongest explanation for carbon sequestration and habitat quality, and the interaction between land use type and precipitation had the strongest interpretation for water yield. The results can provide a theoretical basis for ecological protection and ecological civilization construction in Nagqu and its surrounding areas.